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By the mid 24th century, the clerics believed that the Klingon ideals expressed by the original Kahless had become corrupted, and that the Klingon people had lost their way. Feeling that the people needed a spiritual figure to rally behind, they decided to take genetic material from the original Kahless and create a clone. They programmed the clone with the memories of the original Kahless - including the story of the original bat'leth, which was known only to certain clerics.

The deception was soon exposed when ChancellorGowron defeated Kahless in combat. Worf felt that the Klingon people still needed a symbol, and proposed that the clone become the ceremonial Emperor of the Klingon Empire, the first in 300 years, while the actual power would still rest in the Chancellor and the High Council. (TNGepisode: "Rightful Heir")

In 2379, the Klingon rebel group Klahb took over the Federation Embassy on Qo'noS and demanded, among other things, that the hologram posing as Kahless be deactivated. Until then, Martok and the High Council had been unaware of the duplicity. Many believed that the Federation was responsible for kidnapping Kahless and replacing him. This belief was further fueled by the discovery that the hologram was kept active by a copy of the mobile emitter that the USS Voyager brought back from the Delta Quadrant.

As it turned out, Kahless had replaced himself to see "how long it would take you to notice." The answer turned out to be six months. After getting help from discreet Klingon friends, Kahless traveled to Cygnet IV where he took up painting. He was found by the USS Enterprise-E and taken back to Qo'noS where he told Martok that he was no longer needed. After undergoing the vIt 'Iw tay ritual, he returned to Cygnet IV to allow himself time to be selfish and to do whatever he wanted. (TNG - A Time to...novel: A Time for War, A Time for Peace)

In 2386, Kahless was invited to speak at a ceremony honoring the victors of the battle that had decided the fate of the House of Kruge over a century ago, being transported on the Enterprise-E, but was disgusted when Picard was forced to reveal that actually none of the lords of the House of Kruge had actually fought in the battle themselves. Although still willing to attend the ceremony, Kahless's intention had been to reveal the truths he revealed about the nobility in attendance. He was swiftly abducted by the Unsung, a group of Klingons descended from soldiers who had been defeated in the battle. After being captured, Kahless was then forced to toil in the sewage pits on the Unsung's planet. Kahless was apparently executed by the Unsung. But, this execution was revealed to have been faked by the Circle of Jilaan, a group of con artists who intended to study Kahless and fake the true return of Kahless later to manipulate the Empire for themselves. Despite his captivity, Kahless is able to outmaneuver his captures and escape. Kahless was able to hide within the conduits of the ship where he was being held. He later reunited with Worf while he has been forced to retreat to another planet with the remaining Unsung after Kruge's chosen heir, Korgh, betrays them. Spending time with the Unsung, Kahless is able to teach them what it means to be Klingon and recognize that their discommendation does not mean that they should reject their heritage, most notably when forcing Harch, one of the Unsung, to acknowledge his newborn son. When Korgh's true role in the crisis is exposed, Kahless decides to join the last of the Unsung in their new responsibility as guardians for Spirits' Forge to win back their honor, reflecting that, where the true Kahless leads deserving souls to Sto-Vo-Kor, the clone Kahless will help the living reach a point where they deserve such an honor (Preynovels: Hell's Heart, The Jackal's Trick, The Hall of Heroes).

The following year, with the beginning of the Iconian War, Kahless was revealed to be the head of House Pegh, an elite group of warriors working clandestinely against threats of the Empire. Wielding the Sword of Kahless, the Emperor led a strike team - aided by Federation, Klingon, and Romulan Republic forces - to an Iconian facility dealing in the production of Omega molecules in the Dinasia system. On the surface of Dinasia Prime, he broke away from the main group and the mission plan to challenge the Iconian known as T'ket to single combat, while the strike force attempted to disable the Omega generators. B'Eler discovered that a weakness in the Iconians involving Omega, and temporarily disabled T'ket. Instead of striking the death-blow, Kahless told the Iconian he was victorious because he had honor on his side, at which point T'ket teleported behind him and ran him through. Upon seeing this, Ramir panicked, alerting T'ket to the team's position, and the strike force was forced to flee the planet with only one of three mission objectives successful. (STO - "The Iconian War" mission: "House Pegh")